Midterm 1 Flashcards
Potential Energy
Stored energy, object gains/loses ability to store E based on its position
molecular: related to the position of shared e- in covalent bonds (farther from nucleus = more PE)
Higher up/farther away something is the more potential E
Beige Adipose Tissue (BAT)
Burns E to produce heat (thermogenesis)
Made from WAT (in cold temps)
White Adipose Tissue (WAT)
Stores E
In warm temperatures what cells do mammals make? In cold temperatures what cells do mammals make?
Cold temps = make more beige adipose cells (generate heat to combat cold)
Warm temps = make more white adipose cells to store energy
Kinetic Energy
Energy of motion
molecules have it bc constantly in motion
KE of molecular motion = thermal E
Atom
Extremely small particles called e- orbit an atomic nucleus made of larger particles called protons and neutrons in the nucleus.
Atomic nucleus
Made up of protons and neutrons or 1 proton (hydrogen) surrounded by orbiting electrons
e- more dense in center of nucleus & less as it gets further away (more PE)
What e- have the most PE?
e- in outermost/valence shell (furthest from nucleus) = more potential E
takes more E for e- to be in outer shell than inner one (bc nucleus has + protons that e- attracted to ) & able to do more reactivity outside
Chemical bond
Attractions that bind atoms together
Ion
An atom / molecule that has lost/gained e- and thus, carries a full electrical charge
cation = positive
anion = negative
Ionic bond
e- are completely transferred from one atom to another, e- transfer occurs bc it gives resulting atoms a full valence shell, 2 opposite charged ions (cation +, anion -)
Tends to happen when 1/2 valence e-
Molecule
Substances held together by covalent bonds
Covalent bond
Shared e- “glue” atoms together, a strong attraction where 2 atoms share electrons, no full charge
Nonpolar covalent bonds
e- are shared EQUALLY between 2 atoms in bond (NO PARTIAL CHARGES)
Electroneg diff 0.5>
Store the most PE bc negatively-charged e- are equally far from both atoms’ positively charged atomic nuclei
Positive & Negative charges attract each other -> energetically unfavorable state, takes a large amount of PE for the e- to remain in this position
Polar Covalent bonds
UNEQUAL sharing of e- (e- more close to the nucleus of more electronegative atom)
No full charge
Ex: H2O
1 atom attracts more electron (partially negative) & other atom is partially positive.
Stores the least PE
Energetically favorable
Electroneg difference 0.5<
Negatively-charged e- are far from one atom’s atomic nucleus, & are much closer to the other atom’s atomic nucleus. Bc positive and negative charges attract each other -> energetically favorable state
Does not take much PE for e- to remain in this position
Electron Shells
Electrons can move around atomic nuclei in specific regions called orbitals (can hold up to 2 electrons) & these orbitals are grouped into levels (shells)
What does the numbering of electron shells tell you?
Orbitals are numbered 1, 2, 3 etc. to indicate their distance from the nucleus (small - closer)
What type of electrons are located in the “valence shell”? How does this relate to the “valence” of an atom?
valence e- are located in valence shell & determine reactivity
The outermost e- as not full (at least one orbital w/ unpaired valence e-)
Valence
of unpaired e- in outermost shell
e- in valence shell “like” to be paired
# unpaired e- in outermost shell
Atomic Bonding
Atoms connected by bonds
stable & more happy when outermost shell = full
Electronegativity
When atoms of different elements form a bond, they may pull shared e- towards their nuclei with varying strengths
- large #s = stronger pull (oxygen sucks = highest )
If difference = 1 or large = Higher polarity
When would you consider a bond is nonpolar in terms of electronegativity?
If the difference is less than 0.5 -> has a smaller polarity and means that there is Higher PE
Bond Energy
not actually in orbits but clouds of e-
more energetic e- spend more time in outer shells (Higher PE)
How does the type of bond affect the location of the e- and how much E the bonds have
if e- far from all atomic nuclei = nonpolar (most PE)
e- close to 1 nucleus & far from another = polar (less PE)
e- very close to nucleus = ionic (lowest PE)
Explain why the energy differs between the bonds, using appropriate terminology.
Nonpolar bonds store the most potential energy, because the negatively-charged electrons are equally far from both atoms’ positively charged atomic nuclei. Because positive and negative charges attract each other, this is an energetically unfavorable state, meaning that it takes a large amount of potential energy for the electrons to remain in this position.
Polar bonds store the least potential energy, because although the negatively-charged electrons are far from one atom’s atomic nucleus, they are much closer to the other atom’s atomic nucleus. Because positive and negative charges attract each other, this is an energetically favorable state, meaning that it does not take much potential energy for the electrons to remain in this position.
Compare and contrast the three major types of chemical bonds between atoms by filling out the table below:
Ionic, Nonpolar cov, Polar cov
- ionic, full charge, unequal
-polar, partial charge, unequal
-nonpolar, no charge, equal
In your own words, explain why there is a partial negative charge on the oxygen atom in a water molecule (H2O).
-Oxygen has a higher electronegativity & attracts e- from hydrogen & has a partial negative charge
Reactant
Any of the starting materials in a chemical RXN
Product
Any of the final materials formed in a chemical RXN
Free energy
Measure of the capacity of the system to do work (if NEG = spontaneous EXO)
Entropy
The amount of disorder in a system (or environment)
more possible states
Exergonic reaction
Change in Gibbs free E less than zero (Delta G < 0)
spontaneous
Releases heat/Energy
Increasing entropy (High E-> Low E)
Nonpolar -> Polar bonds
Reactants have higher E & Products = Lower E
Still needs trigger to start (activation energy)
Endergonic RXN
Change in Gibbs free E greater than zero (delta G>0) NON spontaneous
Absorbs/requires a input of E to occur
Decreases Entropy
Reactants = Low E & Products = High E
Can be spontaneous if coupled w/ exergonic RXN
Gibbs free-energy change (ΔG)
E of system that can be converted into work
amount of E that is available may be measured only by how it changes in a RXN
First law of thermodynamics:
E is conserved, cannot be destroyed or created only transformed/transferred
Open System
E can enter/exit if it comes from another syst/leaves to another syst
Everything that is alive, earth, E frm sun
Closed System
Nothing gets in/out
-Universe
Second law of thermodynamics:
Spontaneous RXNs, entropy increases when system & environment = considered
state of Entropy(disorder/spontaneous) of the universe/environ will always increase over time
How is Entropy related to PE & bonds?
Low Entropy = High PE (nonpolar bonds)
High Entropy = Low PE (polar bonds)
When you go from Low entropy to High Entropy what is that considered?
Low -> High entropy = Spontaneous (Exergonic)
High -> Low = non spontaneous (Endergonic)
How to calculate change in gibs free E or delta G?
G of products - G of reactants
if pos = endergonic
if neg = exergonic
Catalyze/catalyst
Proteins are specialized to catalyze / speed up chemical RXNs
proteins (catalyst) = enzyme
Enzyme
A protein that functions as a catalyst
Brings substrates together in a precise orientation that makes reactions more likely
Specific for a single RXN – specificity is a product of the geometry & chemical properties of sites where substrate bind
Substrate
A reactant that interacts w/ a catalyst such as an enzyme or ribozyme in a chemical RXN
A surface on which a cell or organism sits
Active site
The location in an enzyme molecules where substrates (reactant molecules) bind & react
catalysis actually occurs
Transition state
A high-E temporary intermediate state of the reactants during a chemical RXN that must be achieved for the RXN to proceed
enzymes play a key role by stabilizing this transition state, thus facilitating the reaction to proceed more efficiently
Activation energy
The amount of KE required to initiate a chemical RXN specifically the energy required to reach the transition state ( a certain amount of KE, RXNS happen when reactants have enough KE to overcome the activation energy barrier)
KE of molecules is a function of their temperature, RXNs tend to proceed faster at high temps
Activation Energy
Energetically favorable (High E -> Low E, Entropy increases)
required in both exo & endo RXNs
like speed bump
required to make transition state
Lower activation energy barrier = more favorable environ.
Enzymes interact with molecules called ______ by binding them in a special location on the _____ site
Enzymes interact with molecules called substrate by binding to them in a special location on the enzyme called the active site
How do enzymes lower activation energy?
Orient substrate (break/form bonds more easily)
Enzymes might add charge phosphate group (destabilize substrate helps break/form bonds)
Manipulate molecule stretch/bond easier to break/form bonds
Conformational change
Enzymes change shape temporarily = not permanent/doest affect function
What does enzyme names end in?
Ase !!!
The ____ barrier exists because enzymes destabilize bonds in the substrates, forming the _____ site .
The activation energy barrier exists because enzymes destabilize bonds in the substrates, forming the transition site .
Energetic Coupling
In cellular metabolism, E is released from an exergonic RXN (commonly, hydrolysis of ATP) is used to make an endergonic RXN spontaneous
Reduction-oxidation (redox) reactions:
Any chemical RXN that involves either the complete transfer of one or more e- from one reactant to another
or a reciprocal shift in position of shared e- w/ in one or more of the covalent bonds of the reactants
OIL RIG
Oxidation - lose e-
Reduction - gain e-
Adenosine triphosphate (ATP)
A molecule consisting of an adenine base, a sugar/ribose (pentagon), and 3 phosphate groups linked together w/ covalent bonds that have high PE
universally used by cells as monomer of RNA synthesis to store & transfer chemical E
Phosphorylation
Addition of a phosphate group to a molecule/substrate (increase in E)
What do you call a phosphorylated molecule?
An Activated substrate (adds E to reactants in endergonic RXN & can proceed)
Explain how the potential energy stored in a molecule of ATP is different from the potential energy that is stored in nonpolar covalent bonds.
ATP stores energy in an unstable, high-energy bond that is quickly accessible for biological functions (terminal phosphate group thru hydrolysis, releases large E)
NONPOLAR covalent bonds store E stably and require specific reactions to release it (long-term E) do not spontaneously release E like ATP
PE is more evenly distributed within the bond between 2 atoms w/ similar electronegativity
What are 2 main ways to transfer E?
1) Phosphate groups (PO4^-3)
2) Move e- (redox)
ATP Hydrolysis
splits molecules into 2 smaller ones (exergonic, releases E) E released can be used to power endergonic RXNs
Where does the energy from ATP come from? ** IMPORTANT
In the phosphate groups of ATP there are a lot of negative charges that repulse each other, this is an energetically unfavorable state and requires lots of PE to overcome (w/o lots of PE would not stay together) E is NOTTT from position of e- in bonds
BREAKING OFF A PHOSPHATE GROUP = RELEASE E
Explain how phosphorylating a substrate can make an endergonic reaction happen “spontaneously.”
In cellular RXNs, ATP hydrolysis (exergonic) is often coupled w/ an endergonic process
The E released from ATP hydrolysis provides the necessary E to make process energetically favorable
This makes the combined reaction, w/ both exergonic ATP hydrolysis and the endergonic RXN, spontaneous (i.e., having a negative ∆G)xzpg
On the molecule of ATP below, label the adenine, ribose, and phosphate groups, then circle the portion of the molecule that holds the highest potential energy.
Phosphate groups (p circles)
= most E
pentagon = ribose, lots of n = adenine
Solution
A liquid containing 1 or more dissolved solids or gasses in a homogenous mixture
Solvent
any liquid in which one or more solids or gasses can dissolve
Solutes
Any substance that is dissolved in a liquid
Polar
Carrying a partial positive charge on one side of a molecule and a partial negative charge on the other
(still considered uncharged bc no full charge/full exchange of e- like ions)
Generally hydrophilic
Hydrogen bond
A weak interaction between 2 molecules / different parts of the same molecule resulting from the attraction between a hydrogen atom w/ a partial pos charge & another atom (usually O or N) w/ a partial neg charge
Weaker bc dont share/exchange e- only like magnets (easily broken by full charges)
How to know if a molecule can make hydrogen bonds?
Lots of polar bonds/more partial charges
How are hydrogen bonds related to dissolving in water?
If molecule forms lots of H-bonds its easier to dissolve in water if not = difficult
Hydrophilic
Interacting readily w/ water
Typically polar
Hydrophobic
Not readily interacting w/ water/scared of water
Typically NONpolar
Hydrophobic interactions
Very weak interactions between nonpolar molecules / nonpolar regions of the same molecule, when exposed to an aqueous solvent
The surrounding water molecules support these interactions by interacting w/ one another & encapsulating the nonpolar molecules
Aqueous solvent
solvent = water
Plasma membrane/cell membrane
A membrane that surrounds a cell, separating it from the external environment & selectively regulating passage of molecules & ions into & out of the cell, (selectively permeable)
Lipid
Any organic substance that does not dissolve in water, but dissolves well in nonpolar organic solvents
EX: fatty acids, fats, oils, waxes, steroids, phospholipids
Hydrocarbons
An organic molecule that contains only hydrogen & carbon atoms
Fatty acid
A lipid consisting of a hydrocarbon chain bonded at one end to a carboxyl group
used by many organisms to store chemical E
Major component of animal & plant fats & phospholipids
Phospholipid
A class of lipid having a hydrophilic head (including phosphate group) & a hydrophobic tail (two hydrocarbon chains)
Major components of plasma membrane/organelle membranes
Amphipathic
Has both hydrophilic and hydrophobic regions
Phospholipid head
hydroPHILIC loves water
Phospholipid tail
HydroPHOBIC (scared of water)
Why are phospholipid tails on inside of membrane structure?
It is energetically favorable to have tails protected from H2O
What crosses the phospholipid bilayer easily? What does not?
Small nonpolar molecules cross easily bc they can bc nonpolar bonds = hydrophobic (cannot form hydrogen bonds w/ water), this molecule should be able to “dissolve” in the hydrophobic tails of the phospholipid bilayer, and pass through the membrane without assistance
But large, polar molecules = harder to cross bc can form hydrogen bonds in water cannot dissolve in hydrophobic tails
Permeability
Tendency of a structure (e.g. membrane) to allow a given substance to diffuse across it
Selective permeability
Variation in how easily molecules move thru membrane
Small, nonpolar molecules (hydrophobic) move easily by diffusion (no help)
Small/Large/POLAR/ions (charge) = hard to get thru bc repelled by inner membrane barrier REQUIRE HELPERS (transport proteins)
MDMA
“Molly” or “Ecstasy
Lab-made (synthetic) drug that has effects similar to stimulants
Mildly alter visual and time perception
more energetic, alert, having an increased sense of well-being, warmth, and openness toward others
Explain why there is a partial negative charge on the oxygen atom in a water molecule
There is a partial negative charge on the oxygen atom in a water molecule because oxygen has a higher electronegativity value than hydrogen, meaning that the negatively charged electrons are pulled towards the positively charged atomic nucleus of Oxygen, creating a partial negative charge on its atom. The polar bond between Oxygen and Hydrogen means that the electrons are shared unequally.
Diffusion
Spontaneous movement of a substance from one region to another
Often with a net movement from a region of HIGH concentration
-> LOW concentration
Going from High order (low entropy) -> Low order (high entropy)
Concentration gradient
Difference across space (e.g. across a membrane) in the concentration of a dissolved substance
Passive transport
Diffusion of a substance across a membrane, when this event occurs w/ the assistance of membrane proteins its called facilitated diffusion
Osmosis
Diffusion of water across a selectively permeable membrane from a region of lower solute concentration (high water concentration) -> higher solute concentration (low water concentration)
Solute CANNOT pass through the membrane (ex: large/polar molecules)
Hypertonic
Loss of water/shrinkage of the membrane-bound structure/cell
Greater solute concentration outside compared to intracellular solute concentration (water moves from inside-> outside)
Used when the solute is unable to pass thru the membrane
Hypotonic
Results in the uptake of water & swelling./bursting of structure (turgid)
Lower solute concentration intracellular than the solution on the extracellular side of membrane (water moves from outside-> inside)
Used when the solute is unable to pass thru the membrane
Isotonic
If inside cell/vesucle -> no net uptake/loss of water & no effect on the volume of membrane bound structure
SAME solute concentration as the solution on the other side of the membrane (extracellular = intracellular amt of solute)
Transmembrane protein (integral membrane protein)
Any membrane protein that spans the entire lipid bilayer
Channel proteins
Transmembrane protein
Forms a pore in a cell membrane, which may open/close in response to a signal
Structure of most channels allows them to admit just 1/a few types of ions or molecules
Aquaporins
Type of channel protein that facilitates the movement of water (osmosis) across a plasma membrane
Facilitated diffusion
Passive movement (diffusion) of a substance across a membrane w/ the assistance of transmembrane carrier proteins or channel proteins
NO ATP
Carrier proteins
A transmembrane protein that facilitates diffusion of a small molecule across a membrane by a process involving a reversible change in the shape of the protein
aka transporter
Active transport
Movement of ions/molecules across a membrane in a single direction, often against a gradient
Requires E (hydrolysis of ATP) & assistance of a transport protein (pump)
ATP synthase
Enzyme that utilizes the energy from an electrochemical gradient of protons or sodium ions to synthesize ATP in the mitochondrial inner membrane
Has F1 & FO subunit
When ATP Synthase transports protons across a membrane to generate ATP what type of transport is this considered?
When ATP synthase transports protons across a membrane to generate ATP, this is considered PASSIVE transport because protons move from an area of high concentration to low concentration
ATP Synthase F1 Unit
Above the membrane, inside the matrix of the mitochondria
ATP Synthase FO Unit
In the inner mitochondrial membrane, involves KE during rotation (rotation engine)(pipe looking things)
Which of the following aspects of ATP synthesis by the ATP synthase protein complex directly involves kinetic energy?
A) The difference in proton concentration across the membrane.
B) The formation of ATP from ADP and Pi.
C) The rotation of the FO subunit.
D) All of the above directly involve kinetic energy.
C! Rotation of the FO Subunit
Explain why, in this situation, water moves to the right, but the green molecules do not move at all
H2O moves from a high water concentration (low solutes) to a low water concentration (more solutes) but the green molecules cannot cross the selectively permeable membrane, only unbound water molecules are able to diffuse across the membrane during osmosis if a solute cant cross the membrane then any associated water molecules are also prevented from crossing
Which type of bond has the most unequal distribution of electrons?
A) Ionic bond
B) Polar covalent bond
C) Nonpolar covalent bond
D) All have unequal distribution of electrons.
A) Ionic bond
Which of the following best describes a “transition state”?
A) The amount of time that passes as the reactants are transformed into the products of a reaction.
B) The amount of energy required for an endergonic reaction to go forward.
C) The difference in free energy between the reactants and the products.
D) A high-energy intermediate state of reactants.
D) A high-energy intermediate state of reactants
Which of the following describes how the lactase enzyme is catalyzing this reaction?
A) It is interacting with the reactants to increase the activation energy.
B) It is interacting with the reactants to stabilize the transition state.
C) It is lowering the free energy of the products.
D) It is increasing the free energy of the reactants.
B) It is interacting with the reactants to stabilize the transition state.
